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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 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'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 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'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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) 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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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) 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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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) 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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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) 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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 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'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 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'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 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'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 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'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $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' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ), 'gf_id' => 'HOM05D001338', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001338' ), 'data_identifier' => 'HOM05D001338', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001338', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '471', 'num_species' => '35' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG8G11080' => 'aar', 'AL1G56700' => 'aly', 'AL3G19600' => 'aly', 'AL4G20870' => 'aly', 'Aqoxy3G01368' => 'aox', 'Aqoxy3G01371' => 'aox', 'Aqoxy5G02339' => 'aox', 'Aqoxy7G02175' => 'aox', 'Aqoxy7G02176' => 'aox', 'AT1G35150' => 'ath', 'AT2G06500' => 'ath', 'AT2G16040' => 'ath', 'AT3G29638' => 'ath', 'AT3G29794' => 'ath', 'AT4G10200' => 'ath', 'AT5G35475' => 'ath', 'Atru.chr1.2432' => 'acertr', 'Atru.chr10.1126' => 'acertr', 'Atru.chr12.2101' => 'acertr', 'Atru.chr2.1436' => 'acertr', 'AUR62026124' => 'cqu', 'AUR62037832' => 'cqu', 'BcaB01g01626' => 'bca', 'BcaB06g28244' => 'bca', 'BolC1t04120H' => 'bol', 'BolC1t04569H' => 'bol', 'BolC2t08893H' => 'bol', 'C01p46080' => 'bna', 'C02p28520' => 'bna', 'C09p32850' => 'bna', 'CAN.G1005.11' => 'can', 'CAN.G105.19' => 'can', 'CAN.G464.34' => 'can', 'CAN.G80.8' => 'can', 'CANSAT01G0302' => 'cansat', 'CANSAT01G1009' => 'cansat', 'CANSAT01G1407' => 'cansat', 'CANSAT11G0800' => 'cansat', 'CANSAT11G1935' => 'cansat', 'CANSAT11G2147' => 'cansat', 'CANSAT21G0118' => 'cansat', 'CANSAT21G0346' => 'cansat', 'CANSAT21G1695' => 'cansat', 'CANSAT21G1775' => 'cansat', 'CANSAT21G2437' => 'cansat', 'CANSAT35G0728' => 'cansat', 'CANSAT35G0841' => 'cansat', 'CANSAT46G0001' => 'cansat', 'CANSAT46G0003' => 'cansat', 'CANSAT54G1040' => 'cansat', 'CANSAT54G1041' => 'cansat', 'CANSAT56G4418' => 'cansat', 'CANSAT64G0482' => 'cansat', 'CANSAT64G1081' => 'cansat', 'CANSAT64G2348' => 'cansat', 'CANSAT80G1592' => 'cansat', 'CANSAT80G1687' => 'cansat', 'CANSAT80G1793' => 'cansat', 'CARHR034340' => 'chi', 'CARHR034350' => 'chi', 'CARHR048790' => 'chi', 'CARHR098000' => 'chi', 'CARHR103200' => 'chi', 'CARHR116070' => 'chi', 'CARHR117440' => 'chi', 'CARHR128510' => 'chi', 'CARHR128520' => 'chi', 'CARHR144860' => 'chi', 'CARHR149350' => 'chi', 'CARHR178380' => 'chi', 'CARHR184740' => 'chi', 'CARHR184750' => 'chi', 'CARHR217430' => 'chi', 'CARHR217440' => 'chi', 'CARHR217460' => 'chi', 'CARHR252010' => 'chi', 'CARHR256860' => 'chi', 'CARHR257160' => 'chi', 'CARHR257270' => 'chi', 'CARHR289900' => 'chi', 'CARHR290850' => 'chi', 'CARHR293480' => 'chi', 'CiPaw.02G115100' => 'cil', 'CiPaw.04G075300' => 'cil', 'CiPaw.11G014600' => 'cil', 'CiPaw.15G122600' => 'cil', 'CSS0004687' => 'camsi', 'CSS0005716' => 'camsi', 'CSS0006616' => 'camsi', 'CSS0006650' => 'camsi', 'CSS0007608' => 'camsi', 'CSS0011720' => 'camsi', 'CSS0012104' => 'camsi', 'CSS0016533' => 'camsi', 'CSS0023742' => 'camsi', 'CSS0025100' => 'camsi', 'CSS0026998' => 'camsi', 'CSS0027088' => 'camsi', 'CSS0029771' => 'camsi', 'CSS0034678' => 'camsi', 'CSS0039736' => 'camsi', 'CSS0047876' => 'camsi', 'ECA232G0049' => 'eca', 'ECA232G4407' => 'eca', 'ECA233G3047' => 'eca', 'ECA236G1638' => 'eca', 'EL10Ac1g02359' => 'bvu', 'EL10Ac2g04353' => 'bvu', 'EL10Ac3g06626' => 'bvu', 'EL10Ac3g06627' => 'bvu', 'EL10Ac6g13918' => 'bvu', 'EL10Ac6g14130' => 'bvu', 'EL10Ac7g17250' => 'bvu', 'EL10Ac9g22457' => 'bvu', 'EL10As4g23382' => 'bvu', 'FAN01G2426' => 'fan', 'FAN02G0003' => 'fan', 'FAN02G1825' => 'fan', 'FAN02G1953' => 'fan', 'FAN05G1733' => 'fan', 'FAN09G1642' => 'fan', 'FAN09G2301' => 'fan', 'FAN09G2928' => 'fan', 'FAN09G2988' => 'fan', 'FAN13G0481' => 'fan', 'FAN14G5297' => 'fan', 'FAN17G2367' => 'fan', 'FAN20G0374' => 'fan', 'FAN22G0863' => 'fan', 'FAN23G1296' => 'fan', 'FAN23G2271' => 'fan', 'FAN25G1338' => 'fan', 'FAN25G1858' => 'fan', 'FAN26G3443' => 'fan', 'FvH4_1g08761' => 'fve', 'FvH4_1g10851' => 'fve', 'FvH4_1g17271' => 'fve', 'FvH4_1g26762' => 'fve', 'FvH4_2g15031' => 'fve', 'FvH4_2g18762' => 'fve', 'FvH4_2g29241' => 'fve', 'FvH4_2g32571' => 'fve', 'FvH4_4g01531' => 'fve', 'FvH4_4g12942' => 'fve', 'FvH4_4g14421' => 'fve', 'FvH4_4g14431' => 'fve', 'FvH4_4g14434' => 'fve', 'FvH4_5g30891' => 'fve', 'FvH4_6g47641' => 'fve', 'FvH4_6g47642' => 'fve', 'FvH4_7g07902' => 'fve', 'Glyma.12G093566' => 'gma', 'Glyma.14G107400' => 'gma', 'Glyma.14G186200' => 'gma', 'Glyma.18G183000' => 'gma', 'Gohir.A06G101504' => 'ghi', 'Gohir.D05G274450' => 'ghi', 'Gohir.D06G166250' => 'ghi', 'Gorai.009G287700' => 'gra', 'Gorai.010G072400' => 'gra', 'Gorai.010G095100' => 'gra', 'HanXRQChr03g0070731' => 'han', 'HanXRQChr10g0286761' => 'han', 'HanXRQChr11g0321031' => 'han', 'HanXRQChr11g0321041' => 'han', 'Medtr2g048200' => 'mtr', 'Medtr3g074100' => 'mtr', 'Medtr3g095880' => 'mtr', 'Medtr4g010145' => 'mtr', 'Medtr5g020070' => 'mtr', 'Medtr5g056540' => 'mtr', 'Medtr7g006410' => 'mtr', 'Medtr7g063340' => 'mtr', 'Medtr7g088730' => 'mtr', 'Oeu000170.1' => 'oeu', 'Oeu001068.1' => 'oeu', 'Oeu002831.1' => 'oeu', 'Oeu002839.1' => 'oeu', 'Oeu003192.1' => 'oeu', 'Oeu003234.1' => 'oeu', 'Oeu005280.1' => 'oeu', 'Oeu005479.1' => 'oeu', 'Oeu006251.1' => 'oeu', 'Oeu008449.1' => 'oeu', 'Oeu008700.1' => 'oeu', 'Oeu008701.1' => 'oeu', 'Oeu009496.1' => 'oeu', 'Oeu009956.1' => 'oeu', 'Oeu011673.1' => 'oeu', 'Oeu011674.1' => 'oeu', 'Oeu011870.1' => 'oeu', 'Oeu012004.1' => 'oeu', 'Oeu012177.1' => 'oeu', 'Oeu012605.1' => 'oeu', 'Oeu012998.1' => 'oeu', 'Oeu013563.1' => 'oeu', 'Oeu013812.1' => 'oeu', 'Oeu015894.1' => 'oeu', 'Oeu016367.1' => 'oeu', 'Oeu016868.1' => 'oeu', 'Oeu017832.1' => 'oeu', 'Oeu018627.1' => 'oeu', 'Oeu018676.2' => 'oeu', 'Oeu019018.1' => 'oeu', 'Oeu019879.2' => 'oeu', 'Oeu020403.1' => 'oeu', 'Oeu020831.2' => 'oeu', 'Oeu021392.1' => 'oeu', 'Oeu022366.1' => 'oeu', 'Oeu022714.1' => 'oeu', 'Oeu023192.1' => 'oeu', 'Oeu023400.1' => 'oeu', 'Oeu023799.1' => 'oeu', 'Oeu024921.1' => 'oeu', 'Oeu025048.1' => 'oeu', 'Oeu025447.1' => 'oeu', 'Oeu026150.1' => 'oeu', 'Oeu026292.1' => 'oeu', 'Oeu027891.1' => 'oeu', 'Oeu028129.1' => 'oeu', 'Oeu028399.1' => 'oeu', 'Oeu029248.1' => 'oeu', 'Oeu029413.1' => 'oeu', 'Oeu030195.1' => 'oeu', 'Oeu031022.1' => 'oeu', 'Oeu031339.1' => 'oeu', 'Oeu032006.1' => 'oeu', 'Oeu032717.1' => 'oeu', 'Oeu033602.1' => 'oeu', 'Oeu033724.1' => 'oeu', 'Oeu034167.1' => 'oeu', 'Oeu034185.1' => 'oeu', 'Oeu034372.1' => 'oeu', 'Oeu034373.1' => 'oeu', 'Oeu034648.1' => 'oeu', 'Oeu035174.1' => 'oeu', 'Oeu035515.1' => 'oeu', 'Oeu037760.1' => 'oeu', 'Oeu039267.2' => 'oeu', 'Oeu039478.1' => 'oeu', 'Oeu039597.1' => 'oeu', 'Oeu039598.1' => 'oeu', 'Oeu039916.1' => 'oeu', 'Oeu039971.1' => 'oeu', 'Oeu042321.2' => 'oeu', 'Oeu043525.1' => 'oeu', 'Oeu044267.1' => 'oeu', 'Oeu044946.1' => 'oeu', 'Oeu045512.1' => 'oeu', 'Oeu045638.1' => 'oeu', 'Oeu045832.1' => 'oeu', 'Oeu046624.1' => 'oeu', 'Oeu048409.1' => 'oeu', 'Oeu049829.1' => 'oeu', 'Oeu051319.1' => 'oeu', 'Oeu052066.1' => 'oeu', 'Oeu052067.1' => 'oeu', 'Oeu052286.1' => 'oeu', 'Oeu052557.1' => 'oeu', 'Oeu052558.1' => 'oeu', 'Oeu052628.1' => 'oeu', 'Oeu052782.1' => 'oeu', 'Oeu052873.1' => 'oeu', 'Oeu053421.1' => 'oeu', 'Oeu054194.1' => 'oeu', 'Oeu054316.1' => 'oeu', 'Oeu054866.1' => 'oeu', 'Oeu055078.1' => 'oeu', 'Oeu056073.1' => 'oeu', 'Oeu056375.1' => 'oeu', 'Oeu057421.1' => 'oeu', 'Oeu057453.1' => 'oeu', 'Oeu057765.1' => 'oeu', 'Oeu058818.1' => 'oeu', 'Oeu060590.1' => 'oeu', 'Oeu061398.1' => 'oeu', 'Oeu063134.1' => 'oeu', 'Oeu063541.1' => 'oeu', 'Oeu063768.1' => 'oeu', 'Oeu064199.1' => 'oeu', 'Oeu064240.1' => 'oeu', 'Oeu064839.1' => 'oeu', 'PGSC0003DMG400038830' => 'stu', 'PSO017G0847' => 'pso', 'PSO017G2034' => 'pso', 'PSO017G5137' => 'pso', 'PSO063G1472' => 'pso', 'PSO063G2681' => 'pso', 'PSO063G3812' => 'pso', 'PSO063G4296' => 'pso', 'PSO063G4981' => 'pso', 'PSO063G5018' => 'pso', 'PSO063G5722' => 'pso', 'PSO063G6488' => 'pso', 'PSO063G6584' => 'pso', 'PSO063G6596' => 'pso', 'PSO063G7197' => 'pso', 'PSO104G0173' => 'pso', 'PSO135G0743' => 'pso', 'PSO138G0008' => 'pso', 'PSO138G0009' => 'pso', 'PSO138G0010' => 'pso', 'PSO144G0149' => 'pso', 'PSO144G0154' => 'pso', 'PSO170G1703' => 'pso', 'PSO170G2214' => 'pso', 'PSO170G2392' => 'pso', 'PSO170G2686' => 'pso', 'PSO170G3017' => 'pso', 'PSO170G3462' => 'pso', 'PSO170G4086' => 'pso', 'PSO170G4402' => 'pso', 'PSO170G4602' => 'pso', 'PSO210G0436' => 'pso', 'PSO210G1168' => 'pso', 'PSO210G1253' => 'pso', 'PSO210G1522' => 'pso', 'PSO210G1814' => 'pso', 'PSO210G2267' => 'pso', 'PSO210G4276' => 'pso', 'PSO210G5802' => 'pso', 'PSO339G2135' => 'pso', 'PSO339G3227' => 'pso', 'PSO339G3296' => 'pso', 'PSO339G3643' => 'pso', 'PSO339G3749' => 'pso', 'PSO339G5254' => 'pso', 'PSO339G5336' => 'pso', 'PSO384G1406' => 'pso', 'PSO384G1931' => 'pso', 'PSO384G2104' => 'pso', 'PSO384G2524' => 'pso', 'PSO384G4132' => 'pso', 'PSO384G4498' => 'pso', 'PSO386G0185' => 'pso', 'PSO421G0097' => 'pso', 'PSO421G0468' => 'pso', 'PSO461G0028' => 'pso', 'PSO478G0790' => 'pso', 'PSO478G0891' => 'pso', 'PSO478G0924' => 'pso', 'PSO478G1760' => 'pso', 'PSO478G3958' => 'pso', 'PSO478G4662' => 'pso', 'PSO541G0488' => 'pso', 'PSO541G1638' => 'pso', 'PSO541G1789' => 'pso', 'PSO541G2431' => 'pso', 'PSO541G2437' => 'pso', 'PSO541G2490' => 'pso', 'PSO541G4464' => 'pso', 'PSO541G5408' => 'pso', 'PSO675G4675' => 'pso', 'PSO675G4854' => 'pso', 'PSO675G6439' => 'pso', 'PSO675G8898' => 'pso', 'PSO724G0816' => 'pso', 'PSO724G0974' => 'pso', 'PSO724G1135' => 'pso', 'PSO724G1235' => 'pso', 'PSO761G0174' => 'pso', 'PSO764G0071' => 'pso', 'PSO781G0024' => 'pso', 'PSO781G0133' => 'pso', 'PSO781G0138' => 'pso', 'PSO781G0216' => 'pso', 'PSO782G2576' => 'pso', 'PSO782G2771' => 'pso', 'PSO801G0075' => 'pso', 'PSO801G0142' => 'pso', 'PSO801G0680' => 'pso', 'PSO801G0833' => 'pso', 'PSO832G0537' => 'pso', 'PSO832G0837' => 'pso', 'PSO832G0893' => 'pso', 'PSO832G2505' => 'pso', 'PSO832G4176' => 'pso', 'RcHm_v2.0_Chr1g0320361' => 'rch', 'RcHm_v2.0_Chr1g0321011' => 'rch', 'RcHm_v2.0_Chr1g0321921' => 'rch', 'RcHm_v2.0_Chr1g0377611' => 'rch', 'RcHm_v2.0_Chr1g0379061' => 'rch', 'RcHm_v2.0_Chr2g0106921' => 'rch', 'RcHm_v2.0_Chr2g0137341' => 'rch', 'RcHm_v2.0_Chr2g0139651' => 'rch', 'RcHm_v2.0_Chr2g0144921' => 'rch', 'RcHm_v2.0_Chr2g0161851' => 'rch', 'RcHm_v2.0_Chr2g0172511' => 'rch', 'RcHm_v2.0_Chr3g0449931' => 'rch', 'RcHm_v2.0_Chr3g0452101' => 'rch', 'RcHm_v2.0_Chr3g0453321' => 'rch', 'RcHm_v2.0_Chr3g0459421' => 'rch', 'RcHm_v2.0_Chr3g0480551' => 'rch', 'RcHm_v2.0_Chr4g0431861' => 'rch', 'RcHm_v2.0_Chr4g0435271' => 'rch', 'RcHm_v2.0_Chr5g0015121' => 'rch', 'RcHm_v2.0_Chr5g0031951' => 'rch', 'RcHm_v2.0_Chr5g0034331' => 'rch', 'RcHm_v2.0_Chr5g0059431' => 'rch', 'RcHm_v2.0_Chr5g0080901' => 'rch', 'RcHm_v2.0_Chr6g0250061' => 'rch', 'RcHm_v2.0_Chr6g0263321' => 'rch', 'RcHm_v2.0_Chr6g0288531' => 'rch', 'RcHm_v2.0_Chr6g0308901' => 'rch', 'RcHm_v2.0_Chr7g0198801' => 'rch', 'RcHm_v2.0_Chr7g0198811' => 'rch', 'RcHm_v2.0_Chr7g0200001' => 'rch', 'RcHm_v2.0_Chr7g0205811' => 'rch', 'RcHm_v2.0_Chr7g0230921' => 'rch', 'RcHm_v2.0_Chr7g0233981' => 'rch', 'Solyc02g024040.1' => 'sly', 'Solyc02g030430.1' => 'sly', 'Solyc03g071610.1' => 'sly', 'Solyc05g018360.1' => 'sly', 'Solyc05g041510.1' => 'sly', 'Solyc08g023550.1' => 'sly', 'Solyc11g061950.1' => 'sly', 'Sp1g30540' => 'spa', 'Sp1g30600' => 'spa', 'Sp1g32380' => 'spa', 'Sp3g17010' => 'spa', 'Sp3g26050' => 'spa', 'Sp3g26320' => 'spa', 'Sp3g27030' => 'spa', 'Sp3g27040' => 'spa', 'Sp4g06670' => 'spa', 'Sp4g09890' => 'spa', 'Sp4g09900' => 'spa', 'Sp5g13100' => 'spa', 'Sp5g19890' => 'spa', 'Sp6g08540' => 'spa', 'Sp6g14340' => 'spa', 'SpUn0007_0210' => 'spa', 'SpUn0060_0030' => 'spa', 'SpUn1024_0010' => 'spa', 'SpUn1024_0020' => 'spa', 'THA.LOC104804542' => 'tha', 'Thecc.05G058200' => 'tca', 'Thhalv10001096m.g' => 'esa', 'Thhalv10009558m.g' => 'esa', 'Thhalv10009736m.g' => 'esa', 'Thhalv10016048m.g' => 'esa', 'Thhalv10017956m.g' => 'esa', 'TPR.G17453' => 'tpr', 'TPR.G34669' => 'tpr', 'TPR.G35432' => 'tpr', 'TPR.G36571' => 'tpr', 'TWI18G0851' => 'twi', 'TWI18G1324' => 'twi', 'TWI31G0800' => 'twi', 'TWI31G1167' => 'twi', 'TWI73G0975' => 'twi', 'TWI74G0618' => 'twi', 'TWI74G0662' => 'twi', 'TWI74G0957' => 'twi', 'TWI74G1236' => 'twi', 'TWI81G1066' => 'twi', 'Zm00001eb027500' => 'zma', 'Zm00001eb077850' => 'zma', 'Zm00001eb109540' => 'zma', 'Zm00001eb123550' => 'zma', 'Zm00001eb125380' => 'zma', 'Zm00001eb139120' => 'zma', 'Zm00001eb152380' => 'zma', 'Zm00001eb204510' => 'zma', 'Zm00001eb237490' => 'zma', 'Zm00001eb311200' => 'zma', 'Zm00001eb395820' => 'zma', 'Zm00001eb395890' => 'zma', 'Zm00001eb419880' => 'zma', 'Zm00001eb426040' => 'zma' ) $gf_id = 'HOM05D001338' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001338' ) $data_identifier = 'HOM05D001338' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'ath' => (int) 7, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 2, 'bol' => (int) 3, 'bna' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 24, 'chi' => (int) 24, 'cil' => (int) 4, 'camsi' => (int) 16, 'eca' => (int) 4, 'bvu' => (int) 9, 'fan' => (int) 19, 'fve' => (int) 17, 'gma' => (int) 4, 'ghi' => (int) 3, 'gra' => (int) 3, 'han' => (int) 4, 'mtr' => (int) 9, 'oeu' => (int) 108, 'stu' => (int) 1, 'pso' => (int) 94, 'rch' => (int) 33, 'sly' => (int) 7, 'spa' => (int) 19, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 10, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426040' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 0